Loading report..

Highlight Samples

This report has flat image plots that won't be highlighted.
See the documentation for help.

Regex mode off

    Rename Samples

    This report has flat image plots that won't be renamed.
    See the documentation for help.

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      This report has flat image plots that won't be hidden.
      See the documentation for help.

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in Cloudbreak-DVT-rna-seq/_data when this report was generated.


        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.


        Load Settings

        Choose a saved report profile from the dropdown box below:

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.16.dev0

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/ewels/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2023-08-17, 12:00 PDT based on data in: /home/bryan/git/MultiQC_TestData/data/modules/bases2fastq/Cloudbreak-DVT-rna-seq


        bases2fastq

        bases2fastq is used to call sequences from element AVITI sequencing images.DOI: 10.1038/s41587-023-01750-7.

        Sequencing Run basic informations

        table of general QC metrics

        This section shows numbers of some metrics that indicate the quality of each sequencing run.

        Polony numbers: total number of polonies. Each polony yields one read1 and one read2

        Percentage assinged: percentage of reads that has been assigned to any sample

        Percentage Q30: percentage of bases that has >=30 base quality (error rate <= 10^-3)

        Percentage Q40: percentage of bases that has >=40 base quality (error rate <= 10^-4)

        Average Base Quality: average base qualities across all bases

        Yield: total volume of data that has been assigned to any sample

        Read1 Average Length: the average length of Read 1

        Read2 Average Length: the average length of Read 2

        Showing 10/10 rows and 8/8 columns.
        Run Name#PoloniesPercentage AssignedPercentage Q30PercentageQ40Average Base QualityYield(Gb)Read1 Average LengthRead2 Average Length
        DVT-0018__e1b7
        1167357302
        97.4
        95.7
        83.0
        41.9
        169.9
        74.7
        74.7
        DVT-0019__85ac
        1185205473
        97.5
        96.2
        84.6
        42.1
        172.7
        74.7
        74.7
        DVT-0020__f923
        1181820539
        97.6
        96.2
        84.4
        42.1
        172.3
        74.7
        74.7
        DVT-0021__3f2c
        1171649999
        97.6
        96.4
        85.0
        42.2
        170.9
        74.7
        74.7
        DVT-0022__08c4
        1132577164
        97.6
        96.4
        85.4
        42.2
        165.1
        74.7
        74.7
        DVT-0023__38a4
        1155816088
        97.6
        96.7
        86.4
        42.3
        168.5
        74.7
        74.7
        DVT-0024__17cf
        1156007394
        97.6
        96.5
        84.2
        42.1
        168.7
        74.7
        74.7
        DVT-0025__2b41
        1145595740
        97.6
        96.3
        84.0
        42.1
        167.0
        74.7
        74.7
        DVT-0030__8a89
        1150782117
        97.6
        96.4
        84.0
        42.1
        167.9
        74.7
        74.7
        DVT-0031__0e11
        1143365365
        97.6
        96.2
        83.7
        42.0
        166.8
        74.7
        74.7

        Sequencing Run QC metrics

        bar plots of general QC metrics

        This section shows and compare some metrics that indicate the quality of each sequencing run.

        Polony numbers: total number of polonies. Each polony will yield one read1 and one read2 Base Qualities: percentage of bases that has >=30 (blue) or >=40 (black) base qualities Percentage assinged: percentage of reads that has been assigned to any sample Data Yield: the total volume of data that has been assigned to any sample

        loading..

        Base Quality Histogram

        Histogram of base qualities

        This sections plot the base qualities histograms.

        Per base quality histogram plots the distribution of each inidividual base qualities.

        Per read quality histogram plots the distribution of average base quality of each read

        loading..

        Quality statistics by cycle

        Base qualities by cycle

        This section plots the base qualities by each sequencing cycle. You can choose to show either median, mean, percentage Q30 or percentage Q40 of each cycle. Read 1 and Read 2 are separated by a red dashed line, such that we can visualize R1 and R2 qualities in one plot.

        loading..

        Sample basic informations

        table of general QC metrics by sample

        This section shows numbers of some metrics that indicate the quality of each sa,[;e].

        Polony numbers: total number of polonies assigned to this sample. Each polony yields one read1 and one read2

        Percentage Q30: percentage of bases that has >=30 base quality (error rate <= 10^-3)

        Percentage Q40: percentage of bases that has >=40 base quality (error rate <= 10^-4)

        Average Base Quality: average base qualities across all bases

        Yield: total volume of data that has been assigned to any sample

        Read1 Average Length: the average length of Read 1

        Read2 Average Length: the average length of Read 2

        Group: A group tag for assigning colors in the plot. The default group of each sample will be their sequencing run name. To customize group tags, you can either

        1) Set the project name when running bases2fastq. In this case the group tags will be project name.

        2) Generate a csv file that has the columns "Run Name","Sample Name" and "Group". An easy way of generating this csv will be run multiqc with default grouping, copy this table into a csv file, and then change group name manually. Then move the csv file into any location under the analyzed directory.

        Showing 160/160 rows and 9/9 columns.
        Sample NameRun Name#PoloniesPercentage Q30Percentage Q40Average Base QualityYield(Gb)Read1 Average LengthRead2 Average LengthGroup
        DVT-0018__e1b7__RNASeqPool1-1
        DVT-0018__e1b7
        76698251
        95.8
        83.2
        41.0
        11.4
        74.6
        74.6
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool1-2
        DVT-0018__e1b7
        63936739
        95.7
        83.0
        41.0
        9.6
        74.7
        74.7
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool1-3
        DVT-0018__e1b7
        62280941
        96.0
        83.6
        41.1
        9.3
        74.8
        74.8
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool1-4
        DVT-0018__e1b7
        75528887
        95.7
        83.0
        41.0
        11.3
        74.7
        74.7
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool1-5
        DVT-0018__e1b7
        71493319
        95.7
        82.8
        40.9
        10.7
        74.5
        74.5
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool1-6
        DVT-0018__e1b7
        73428641
        95.7
        83.1
        41.0
        11.0
        74.7
        74.7
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool1-7
        DVT-0018__e1b7
        74465844
        95.8
        83.5
        41.0
        11.1
        74.7
        74.7
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool1-8
        DVT-0018__e1b7
        74786620
        95.9
        83.5
        41.1
        11.2
        74.7
        74.7
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool2-1
        DVT-0018__e1b7
        72751976
        95.9
        83.6
        41.1
        10.9
        74.7
        74.7
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool2-2
        DVT-0018__e1b7
        66583138
        95.7
        82.8
        40.9
        9.9
        74.7
        74.7
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool2-3
        DVT-0018__e1b7
        62117824
        96.0
        83.7
        41.1
        9.3
        74.8
        74.8
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool2-4
        DVT-0018__e1b7
        63527063
        96.0
        83.6
        41.1
        9.5
        74.7
        74.7
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool2-5
        DVT-0018__e1b7
        70979804
        95.8
        83.0
        41.0
        10.6
        74.7
        74.7
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool2-6
        DVT-0018__e1b7
        76096049
        95.9
        83.3
        41.0
        11.4
        74.7
        74.7
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool2-7
        DVT-0018__e1b7
        71748211
        95.6
        82.6
        40.9
        10.7
        74.7
        74.7
        DVT-0018__e1b7
        DVT-0018__e1b7__RNASeqPool2-8
        DVT-0018__e1b7
        75128522
        95.6
        82.5
        40.8
        11.2
        74.7
        74.7
        DVT-0018__e1b7
        DVT-0019__85ac__RNASeqPool1-1
        DVT-0019__85ac
        77943470
        96.3
        84.8
        41.3
        11.6
        74.6
        74.6
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool1-2
        DVT-0019__85ac
        65010928
        96.2
        84.6
        41.3
        9.7
        74.7
        74.7
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool1-3
        DVT-0019__85ac
        63218488
        96.4
        85.2
        41.4
        9.5
        74.8
        74.8
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool1-4
        DVT-0019__85ac
        76745404
        96.2
        84.5
        41.3
        11.5
        74.7
        74.7
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool1-5
        DVT-0019__85ac
        72709794
        96.2
        84.4
        41.2
        10.8
        74.5
        74.5
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool1-6
        DVT-0019__85ac
        74564836
        96.2
        84.6
        41.3
        11.1
        74.7
        74.7
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool1-7
        DVT-0019__85ac
        75591040
        96.3
        85.0
        41.4
        11.3
        74.7
        74.7
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool1-8
        DVT-0019__85ac
        76085258
        96.3
        85.0
        41.4
        11.4
        74.7
        74.7
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool2-1
        DVT-0019__85ac
        73851933
        96.4
        85.1
        41.4
        11.0
        74.7
        74.7
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool2-2
        DVT-0019__85ac
        67711789
        96.1
        84.3
        41.2
        10.1
        74.7
        74.7
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool2-3
        DVT-0019__85ac
        63128624
        96.4
        85.2
        41.4
        9.4
        74.8
        74.8
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool2-4
        DVT-0019__85ac
        64522152
        96.4
        85.1
        41.4
        9.6
        74.7
        74.7
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool2-5
        DVT-0019__85ac
        72230705
        96.2
        84.6
        41.3
        10.8
        74.7
        74.7
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool2-6
        DVT-0019__85ac
        77314784
        96.3
        84.8
        41.4
        11.6
        74.7
        74.7
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool2-7
        DVT-0019__85ac
        72873313
        96.1
        84.2
        41.2
        10.9
        74.7
        74.7
        DVT-0019__85ac
        DVT-0019__85ac__RNASeqPool2-8
        DVT-0019__85ac
        76395791
        96.0
        84.0
        41.2
        11.4
        74.7
        74.7
        DVT-0019__85ac
        DVT-0020__f923__RNASeqPool1-1
        DVT-0020__f923
        77759803
        96.3
        84.6
        41.4
        11.6
        74.6
        74.6
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool1-2
        DVT-0020__f923
        64842870
        96.2
        84.3
        41.3
        9.7
        74.7
        74.7
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool1-3
        DVT-0020__f923
        63137549
        96.4
        84.9
        41.5
        9.4
        74.8
        74.8
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool1-4
        DVT-0020__f923
        76534163
        96.2
        84.3
        41.3
        11.4
        74.7
        74.7
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool1-5
        DVT-0020__f923
        72803181
        96.2
        84.2
        41.3
        10.9
        74.5
        74.5
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool1-6
        DVT-0020__f923
        74288687
        96.2
        84.3
        41.3
        11.1
        74.7
        74.7
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool1-7
        DVT-0020__f923
        75348646
        96.3
        84.8
        41.4
        11.3
        74.7
        74.7
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool1-8
        DVT-0020__f923
        75958801
        96.3
        84.7
        41.4
        11.3
        74.7
        74.7
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool2-1
        DVT-0020__f923
        73638504
        96.4
        84.9
        41.5
        11.0
        74.7
        74.7
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool2-2
        DVT-0020__f923
        67723051
        96.2
        84.2
        41.3
        10.1
        74.7
        74.7
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool2-3
        DVT-0020__f923
        63018922
        96.4
        84.9
        41.5
        9.4
        74.8
        74.8
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool2-4
        DVT-0020__f923
        64271926
        96.4
        84.8
        41.4
        9.6
        74.7
        74.7
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool2-5
        DVT-0020__f923
        72109469
        96.2
        84.3
        41.3
        10.8
        74.7
        74.7
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool2-6
        DVT-0020__f923
        77148909
        96.3
        84.6
        41.4
        11.5
        74.7
        74.7
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool2-7
        DVT-0020__f923
        72469640
        96.1
        83.9
        41.2
        10.8
        74.7
        74.7
        DVT-0020__f923
        DVT-0020__f923__RNASeqPool2-8
        DVT-0020__f923
        76236256
        96.0
        83.8
        41.2
        11.4
        74.7
        74.7
        DVT-0020__f923
        DVT-0021__3f2c__RNASeqPool1-1
        DVT-0021__3f2c
        77073578
        96.5
        85.3
        41.5
        11.5
        74.6
        74.6
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool1-2
        DVT-0021__3f2c
        64334051
        96.3
        85.0
        41.4
        9.6
        74.7
        74.7
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool1-3
        DVT-0021__3f2c
        62591396
        96.6
        85.6
        41.6
        9.4
        74.8
        74.8
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool1-4
        DVT-0021__3f2c
        75902569
        96.4
        85.0
        41.4
        11.3
        74.7
        74.7
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool1-5
        DVT-0021__3f2c
        72141232
        96.3
        84.8
        41.4
        10.8
        74.5
        74.5
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool1-6
        DVT-0021__3f2c
        73714995
        96.4
        85.0
        41.4
        11.0
        74.7
        74.7
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool1-7
        DVT-0021__3f2c
        74686832
        96.5
        85.4
        41.5
        11.2
        74.7
        74.7
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool1-8
        DVT-0021__3f2c
        75336092
        96.5
        85.4
        41.5
        11.2
        74.7
        74.7
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool2-1
        DVT-0021__3f2c
        73004947
        96.6
        85.6
        41.6
        10.9
        74.7
        74.7
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool2-2
        DVT-0021__3f2c
        67101713
        96.4
        84.8
        41.4
        10.0
        74.7
        74.7
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool2-3
        DVT-0021__3f2c
        62390524
        96.6
        85.6
        41.6
        9.3
        74.8
        74.8
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool2-4
        DVT-0021__3f2c
        63724913
        96.5
        85.4
        41.5
        9.5
        74.7
        74.7
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool2-5
        DVT-0021__3f2c
        71468668
        96.4
        85.0
        41.4
        10.7
        74.7
        74.7
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool2-6
        DVT-0021__3f2c
        76547312
        96.5
        85.3
        41.5
        11.4
        74.7
        74.7
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool2-7
        DVT-0021__3f2c
        72039231
        96.2
        84.6
        41.3
        10.8
        74.7
        74.7
        DVT-0021__3f2c
        DVT-0021__3f2c__RNASeqPool2-8
        DVT-0021__3f2c
        75517513
        96.2
        84.4
        41.3
        11.3
        74.7
        74.7
        DVT-0021__3f2c
        DVT-0022__08c4__RNASeqPool1-1
        DVT-0022__08c4
        74480325
        96.5
        85.7
        41.5
        11.1
        74.6
        74.6
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool1-2
        DVT-0022__08c4
        62159732
        96.4
        85.4
        41.5
        9.3
        74.7
        74.7
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool1-3
        DVT-0022__08c4
        60568480
        96.7
        86.0
        41.6
        9.1
        74.8
        74.8
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool1-4
        DVT-0022__08c4
        73225396
        96.5
        85.4
        41.5
        10.9
        74.7
        74.7
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool1-5
        DVT-0022__08c4
        69473906
        96.4
        85.3
        41.5
        10.4
        74.5
        74.5
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool1-6
        DVT-0022__08c4
        71142887
        96.4
        85.4
        41.5
        10.6
        74.7
        74.7
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool1-7
        DVT-0022__08c4
        72222698
        96.5
        85.8
        41.6
        10.8
        74.7
        74.7
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool1-8
        DVT-0022__08c4
        72790289
        96.6
        85.8
        41.6
        10.9
        74.7
        74.7
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool2-1
        DVT-0022__08c4
        70625410
        96.6
        86.0
        41.6
        10.5
        74.7
        74.7
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool2-2
        DVT-0022__08c4
        64811666
        96.4
        85.3
        41.5
        9.7
        74.7
        74.7
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool2-3
        DVT-0022__08c4
        60378502
        96.7
        86.0
        41.6
        9.0
        74.8
        74.8
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool2-4
        DVT-0022__08c4
        61533928
        96.6
        85.9
        41.6
        9.2
        74.7
        74.7
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool2-5
        DVT-0022__08c4
        69255187
        96.5
        85.5
        41.5
        10.3
        74.7
        74.7
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool2-6
        DVT-0022__08c4
        73882078
        96.6
        85.7
        41.5
        11.0
        74.7
        74.7
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool2-7
        DVT-0022__08c4
        69490309
        96.3
        85.0
        41.4
        10.4
        74.7
        74.7
        DVT-0022__08c4
        DVT-0022__08c4__RNASeqPool2-8
        DVT-0022__08c4
        73032846
        96.3
        84.9
        41.4
        10.9
        74.7
        74.7
        DVT-0022__08c4
        DVT-0023__38a4__RNASeqPool1-1
        DVT-0023__38a4
        76022993
        96.8
        86.6
        41.7
        11.3
        74.6
        74.6
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool1-2
        DVT-0023__38a4
        63457772
        96.7
        86.3
        41.6
        9.5
        74.7
        74.7
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool1-3
        DVT-0023__38a4
        61740635
        96.9
        87.0
        41.8
        9.2
        74.8
        74.8
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool1-4
        DVT-0023__38a4
        74857598
        96.7
        86.4
        41.7
        11.2
        74.7
        74.7
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool1-5
        DVT-0023__38a4
        71145923
        96.7
        86.2
        41.6
        10.6
        74.5
        74.5
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool1-6
        DVT-0023__38a4
        72690755
        96.7
        86.3
        41.6
        10.9
        74.7
        74.7
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool1-7
        DVT-0023__38a4
        73701411
        96.8
        86.7
        41.7
        11.0
        74.7
        74.7
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool1-8
        DVT-0023__38a4
        74335791
        96.8
        86.7
        41.7
        11.1
        74.7
        74.7
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool2-1
        DVT-0023__38a4
        71985634
        96.9
        86.9
        41.8
        10.8
        74.7
        74.7
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool2-2
        DVT-0023__38a4
        66189739
        96.7
        86.3
        41.6
        9.9
        74.7
        74.7
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool2-3
        DVT-0023__38a4
        61559388
        96.9
        86.9
        41.8
        9.2
        74.8
        74.8
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool2-4
        DVT-0023__38a4
        62870639
        96.9
        86.7
        41.7
        9.4
        74.7
        74.7
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool2-5
        DVT-0023__38a4
        70443050
        96.7
        86.4
        41.7
        10.5
        74.7
        74.7
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool2-6
        DVT-0023__38a4
        75508630
        96.8
        86.6
        41.7
        11.3
        74.7
        74.7
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool2-7
        DVT-0023__38a4
        71044289
        96.6
        86.0
        41.6
        10.6
        74.7
        74.7
        DVT-0023__38a4
        DVT-0023__38a4__RNASeqPool2-8
        DVT-0023__38a4
        74497709
        96.6
        85.9
        41.5
        11.1
        74.7
        74.7
        DVT-0023__38a4
        DVT-0024__17cf__RNASeqPool1-1
        DVT-0024__17cf
        75998363
        96.5
        84.4
        41.4
        11.3
        74.7
        74.7
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool1-2
        DVT-0024__17cf
        63425309
        96.4
        84.2
        41.3
        9.5
        74.7
        74.7
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool1-3
        DVT-0024__17cf
        61889223
        96.7
        84.8
        41.5
        9.3
        74.8
        74.8
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool1-4
        DVT-0024__17cf
        74892520
        96.5
        84.1
        41.4
        11.2
        74.7
        74.7
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool1-5
        DVT-0024__17cf
        71084094
        96.4
        83.9
        41.3
        10.6
        74.5
        74.5
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool1-6
        DVT-0024__17cf
        72611020
        96.4
        84.1
        41.3
        10.9
        74.7
        74.7
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool1-7
        DVT-0024__17cf
        73690212
        96.6
        84.6
        41.4
        11.0
        74.7
        74.7
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool1-8
        DVT-0024__17cf
        74346531
        96.6
        84.6
        41.5
        11.1
        74.7
        74.7
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool2-1
        DVT-0024__17cf
        72036601
        96.7
        84.8
        41.5
        10.8
        74.7
        74.7
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool2-2
        DVT-0024__17cf
        66280906
        96.4
        83.9
        41.3
        9.9
        74.7
        74.7
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool2-3
        DVT-0024__17cf
        61815921
        96.7
        84.8
        41.5
        9.2
        74.8
        74.8
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool2-4
        DVT-0024__17cf
        62923835
        96.6
        84.6
        41.5
        9.4
        74.7
        74.7
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool2-5
        DVT-0024__17cf
        70556932
        96.5
        84.1
        41.3
        10.5
        74.7
        74.7
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool2-6
        DVT-0024__17cf
        75504787
        96.6
        84.4
        41.4
        11.3
        74.7
        74.7
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool2-7
        DVT-0024__17cf
        70952308
        96.3
        83.6
        41.2
        10.6
        74.7
        74.7
        DVT-0024__17cf
        DVT-0024__17cf__RNASeqPool2-8
        DVT-0024__17cf
        74685598
        96.3
        83.5
        41.2
        11.2
        74.7
        74.7
        DVT-0024__17cf
        DVT-0025__2b41__RNASeqPool1-1
        DVT-0025__2b41
        75335790
        96.4
        84.2
        41.4
        11.2
        74.6
        74.6
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool1-2
        DVT-0025__2b41
        62837630
        96.3
        84.0
        41.3
        9.4
        74.7
        74.7
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool1-3
        DVT-0025__2b41
        61329500
        96.6
        84.6
        41.4
        9.2
        74.8
        74.8
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool1-4
        DVT-0025__2b41
        74105169
        96.3
        83.9
        41.3
        11.1
        74.7
        74.7
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool1-5
        DVT-0025__2b41
        70180527
        96.3
        83.7
        41.3
        10.5
        74.5
        74.5
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool1-6
        DVT-0025__2b41
        72018241
        96.3
        83.9
        41.3
        10.8
        74.7
        74.7
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool1-7
        DVT-0025__2b41
        73086533
        96.5
        84.5
        41.4
        10.9
        74.7
        74.7
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool1-8
        DVT-0025__2b41
        73704499
        96.5
        84.4
        41.4
        11.0
        74.7
        74.7
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool2-1
        DVT-0025__2b41
        71426745
        96.5
        84.5
        41.4
        10.7
        74.7
        74.7
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool2-2
        DVT-0025__2b41
        65563532
        96.3
        83.7
        41.3
        9.8
        74.7
        74.7
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool2-3
        DVT-0025__2b41
        61196718
        96.6
        84.6
        41.5
        9.2
        74.8
        74.8
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool2-4
        DVT-0025__2b41
        62367586
        96.5
        84.4
        41.4
        9.3
        74.7
        74.7
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool2-5
        DVT-0025__2b41
        69858954
        96.4
        83.9
        41.3
        10.4
        74.7
        74.7
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool2-6
        DVT-0025__2b41
        74752754
        96.5
        84.2
        41.4
        11.2
        74.7
        74.7
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool2-7
        DVT-0025__2b41
        70419881
        96.2
        83.5
        41.2
        10.5
        74.7
        74.7
        DVT-0025__2b41
        DVT-0025__2b41__RNASeqPool2-8
        DVT-0025__2b41
        73932804
        96.2
        83.4
        41.2
        11.1
        74.7
        74.7
        DVT-0025__2b41
        DVT-0030__8a89__RNASeqPool1-1
        DVT-0030__8a89
        75017757
        96.5
        84.3
        41.4
        11.2
        74.6
        74.6
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool1-2
        DVT-0030__8a89
        62531267
        96.4
        84.1
        41.3
        9.3
        74.7
        74.7
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool1-3
        DVT-0030__8a89
        61279537
        96.6
        84.7
        41.5
        9.2
        74.8
        74.8
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool1-4
        DVT-0030__8a89
        73790830
        96.4
        84.1
        41.3
        11.0
        74.7
        74.7
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool1-5
        DVT-0030__8a89
        70102951
        96.4
        83.9
        41.3
        10.5
        74.5
        74.5
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool1-6
        DVT-0030__8a89
        71701883
        96.4
        84.1
        41.3
        10.7
        74.7
        74.7
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool1-7
        DVT-0030__8a89
        72766413
        96.5
        84.6
        41.4
        10.9
        74.7
        74.7
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool1-8
        DVT-0030__8a89
        73358425
        96.6
        84.5
        41.4
        11.0
        74.7
        74.7
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool2-1
        DVT-0030__8a89
        71313177
        96.6
        84.6
        41.5
        10.7
        74.7
        74.7
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool2-2
        DVT-0030__8a89
        65526097
        96.4
        83.8
        41.3
        9.8
        74.7
        74.7
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool2-3
        DVT-0030__8a89
        61269219
        96.6
        84.7
        41.5
        9.2
        74.8
        74.8
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool2-4
        DVT-0030__8a89
        62201663
        96.6
        84.6
        41.5
        9.3
        74.7
        74.7
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool2-5
        DVT-0030__8a89
        70223194
        96.4
        84.0
        41.3
        10.5
        74.7
        74.7
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool2-6
        DVT-0030__8a89
        74371000
        96.5
        84.3
        41.4
        11.1
        74.7
        74.7
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool2-7
        DVT-0030__8a89
        69877507
        96.3
        83.6
        41.2
        10.4
        74.7
        74.7
        DVT-0030__8a89
        DVT-0030__8a89__RNASeqPool2-8
        DVT-0030__8a89
        73643799
        96.2
        83.5
        41.2
        11.0
        74.7
        74.7
        DVT-0030__8a89
        DVT-0031__0e11__RNASeqPool1-1
        DVT-0031__0e11
        74591168
        96.3
        84.0
        41.3
        11.1
        74.6
        74.6
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool1-2
        DVT-0031__0e11
        62122702
        96.2
        83.8
        41.2
        9.3
        74.7
        74.7
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool1-3
        DVT-0031__0e11
        60974793
        96.5
        84.4
        41.4
        9.1
        74.8
        74.8
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool1-4
        DVT-0031__0e11
        73306419
        96.3
        83.7
        41.2
        10.9
        74.7
        74.7
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool1-5
        DVT-0031__0e11
        69448126
        96.2
        83.5
        41.2
        10.4
        74.5
        74.5
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool1-6
        DVT-0031__0e11
        71245571
        96.2
        83.7
        41.2
        10.6
        74.7
        74.7
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool1-7
        DVT-0031__0e11
        72329037
        96.4
        84.2
        41.3
        10.8
        74.7
        74.7
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool1-8
        DVT-0031__0e11
        72834795
        96.4
        84.2
        41.3
        10.9
        74.7
        74.7
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool2-1
        DVT-0031__0e11
        70958066
        96.5
        84.4
        41.4
        10.6
        74.7
        74.7
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool2-2
        DVT-0031__0e11
        65058933
        96.2
        83.5
        41.2
        9.7
        74.7
        74.7
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool2-3
        DVT-0031__0e11
        60844745
        96.5
        84.4
        41.4
        9.1
        74.8
        74.8
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool2-4
        DVT-0031__0e11
        61741531
        96.4
        84.2
        41.3
        9.2
        74.7
        74.7
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool2-5
        DVT-0031__0e11
        69610166
        96.3
        83.7
        41.2
        10.4
        74.7
        74.7
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool2-6
        DVT-0031__0e11
        73957429
        96.4
        84.0
        41.3
        11.1
        74.7
        74.7
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool2-7
        DVT-0031__0e11
        69589820
        96.1
        83.3
        41.1
        10.4
        74.7
        74.7
        DVT-0031__0e11
        DVT-0031__0e11__RNASeqPool2-8
        DVT-0031__0e11
        73218583
        96.1
        83.1
        41.1
        10.9
        74.7
        74.7
        DVT-0031__0e11

        Adapter Content

        The plot of adapter content by cycle

        This section plots the adapter content percentage by cycles

        loading..

        Per Cycle Sequence Composition

        The proportion of each base position for which each of the four normal DNA bases has been called.

        The heatmap is formatted in a similar way as fastqc per base sequence content. The differences are: 1) The pass/fail flag in the original fastqc module are replaced with a color reflecting the group tag of the samples 2) Read1 and Read2 is co-plotted and separate by a white band in the heatmap and a red dashed in each individual sample plot.

        The following is a copy of helptext of the fastqc module: To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Cycle N Content

        N content by cycle

        This section plots the percentage of unidentified bases ("N" bases) by each sequencing cycle. Read 1 and Read 2 are separated by a red dashed line

        loading..

        GC histogram

        The histogram of distributions of percentage GC in each read

        This section plots the distribution of percentage GC in each reads (range: 0-100)

        loading..